Nicola is screwed. She can't afford to withdraw the whip from nine rebels as she will lose her working majority. She can't really discipline them at all as self-ID was not in the SNP manifesto! So she has to do nothing which means they suffer no ill consequences so they will feel braver going forward and more might now join them next time around.
So if you have SNP MSPs, write to them to ask them why they support a bill that is so full of holes when they were not elected on a platform for self-ID!